Locus 716

Sequence ID 2L_DroMel_CAF1
Location 2,084,758 – 2,084,935
Length 177
Max. P 0.992479
window1172 window1173 window1174 window1175

overview

Window 2

Location 2,084,758 – 2,084,870
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.91
Mean single sequence MFE -39.47
Consensus MFE -26.21
Energy contribution -26.43
Covariance contribution 0.22
Combinations/Pair 1.09
Mean z-score -2.57
Structure conservation index 0.66
SVM decision value 1.08
SVM RNA-class probability 0.912708
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2084758 112 + 22407834
AUAAAACUUUGCCGCCUCGAUUGAUUGAUGUGGCCUGGCAUUUGCCAGGUAAUCAGAGGCCAAGGAACCAACCUGUAAGCC--------AGAGUCCUUUGCAAAGGACCUCCUGGCCAAG
......(((((..(((((.......((((...(((((((....))))))).)))))))))))))).............(((--------((.((((((....))))))...))))).... ( -42.01)
>DroSec_CAF1 101889 119 + 1
AUAAAACUUUGCCGCCACGAUUGAUUGAUGUGGCCUGGCAUUUGCCAGGUAAUCAGAGGCCAAGGAAACAACCUGGAAGCCAAGGAGCUAGAGUCCU-AGCGAAGGACCUCCUGGCCAAG
......(((.(((............((((...(((((((....))))))).))))((((((..(....)..(((((...)).))).(((((....))-)))...)).))))..))).))) ( -43.20)
>DroSim_CAF1 101700 119 + 1
AUAAAACUUUGCCGCCUCGAUUGAUUGAUGUGGCCUGGCAUUUGCCAGGUAAUCAGAGGCCAAGGAAACAACCUGGAAGCCAAGGAGCCAGAGUCCU-GGCGAAGGACCUCCUGGCCAAG
......(((.((((((((.......((((...(((((((....))))))).)))))))))..((((......((((...(....)..)))).(((((-.....))))).))))))).))) ( -47.01)
>DroEre_CAF1 104398 99 + 1
AUAAAACUUUGCCGCCUCGAUUGAUUGAUGUGGCCAGGCAUUUGCCAGGUAAUCAGAGGCCAAGGAAGCGACCUGGAAGCAAAGGA---------------------GCUCCUGGCCAAG
.....((((.(((((.((((....)))).)))))..(((....))))))).......(((((.(((.((..(((........))).---------------------))))))))))... ( -35.30)
>DroYak_CAF1 105991 100 + 1
AUAAAACUUUGCCGCCUCGAUUGAUUGAUGUGGCCUGGCAUUUGCCAGGUAAUCAGAGGCCAAGGAAACGACCUGGAAGCCAGGGU--------C------------CCUCUUGGCCAAG
..........(((((.((((....)))).)))))(((((....))))).........((((((((......(((((...)))))..--------.------------..))))))))... ( -39.70)
>DroAna_CAF1 101244 99 + 1
AUAAAAGUUUGCCGCCUCGAUUGAUUGAUGUGGCCAGGCAUUUGCCAGGUAAUCAAUGGCCAAGGAUGCC-CGUCGAUGCCA--------------------AAGGACCUUCUGGCCAUG
......(((((((((.((((....)))).)))).)))))....((((((...((..((((....(((...-.)))...))))--------------------...))...)))))).... ( -29.60)
>consensus
AUAAAACUUUGCCGCCUCGAUUGAUUGAUGUGGCCUGGCAUUUGCCAGGUAAUCAGAGGCCAAGGAAACAACCUGGAAGCCAAGGA________C_______AAGGACCUCCUGGCCAAG
..........(((((.((((....)))).)))))(((((....))))).........(((((.(((...........................................))))))))... (-26.21 = -26.43 +   0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,084,758 – 2,084,870
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.91
Mean single sequence MFE -38.04
Consensus MFE -22.76
Energy contribution -24.95
Covariance contribution 2.20
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 0.60
SVM decision value 0.70
SVM RNA-class probability 0.825871
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2084758 112 - 22407834
CUUGGCCAGGAGGUCCUUUGCAAAGGACUCU--------GGCUUACAGGUUGGUUCCUUGGCCUCUGAUUACCUGGCAAAUGCCAGGCCACAUCAAUCAAUCGAGGCGGCAAAGUUUUAU
...((((....))))((((((.(((((..(.--------.(((....)))..).))))).(((((((((..((((((....))))))....)))).......))))).))))))...... ( -41.71)
>DroSec_CAF1 101889 119 - 1
CUUGGCCAGGAGGUCCUUCGCU-AGGACUCUAGCUCCUUGGCUUCCAGGUUGUUUCCUUGGCCUCUGAUUACCUGGCAAAUGCCAGGCCACAUCAAUCAAUCGUGGCGGCAAAGUUUUAU
...((((((((((((....(((-((....))))).....)))))))(((......)))))))).........(((((....)))))(((((...........)))))............. ( -42.80)
>DroSim_CAF1 101700 119 - 1
CUUGGCCAGGAGGUCCUUCGCC-AGGACUCUGGCUCCUUGGCUUCCAGGUUGUUUCCUUGGCCUCUGAUUACCUGGCAAAUGCCAGGCCACAUCAAUCAAUCGAGGCGGCAAAGUUUUAU
(((.(((.(((((((....(((-((....))))).....)))))))(((......)))..(((((((((..((((((....))))))....)))).......)))))))).)))...... ( -45.61)
>DroEre_CAF1 104398 99 - 1
CUUGGCCAGGAGC---------------------UCCUUUGCUUCCAGGUCGCUUCCUUGGCCUCUGAUUACCUGGCAAAUGCCUGGCCACAUCAAUCAAUCGAGGCGGCAAAGUUUUAU
...((((.(((((---------------------......)).))).))))(((.((((((....((((..((.(((....))).))....)))).....)))))).))).......... ( -31.30)
>DroYak_CAF1 105991 100 - 1
CUUGGCCAAGAGG------------G--------ACCCUGGCUUCCAGGUCGUUUCCUUGGCCUCUGAUUACCUGGCAAAUGCCAGGCCACAUCAAUCAAUCGAGGCGGCAAAGUUUUAU
...(((((((.(.------------.--------(((((((...)))))..))..))))))))..((((..((((((....))))))....)))).......(((((......))))).. ( -38.70)
>DroAna_CAF1 101244 99 - 1
CAUGGCCAGAAGGUCCUU--------------------UGGCAUCGACG-GGCAUCCUUGGCCAUUGAUUACCUGGCAAAUGCCUGGCCACAUCAAUCAAUCGAGGCGGCAAACUUUUAU
.((((((((...((((.(--------------------((....))).)-)))....)))))))).........(((....)))..(((.(.((........)).).))).......... ( -28.10)
>consensus
CUUGGCCAGGAGGUCCUU_______G________UCCUUGGCUUCCAGGUUGUUUCCUUGGCCUCUGAUUACCUGGCAAAUGCCAGGCCACAUCAAUCAAUCGAGGCGGCAAAGUUUUAU
....(((.(((((((........................)))))))..............(((((((((..((((((....))))))....)))).......)))))))).......... (-22.76 = -24.95 +   2.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,084,798 – 2,084,907
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.92
Mean single sequence MFE -36.00
Consensus MFE -21.24
Energy contribution -21.97
Covariance contribution 0.72
Combinations/Pair 1.21
Mean z-score -2.71
Structure conservation index 0.59
SVM decision value 2.33
SVM RNA-class probability 0.992479
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2084798 109 - 22407834
UA--UAAAUAUCC-AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUUUGCAAAGGACUCU--------GGCUUACAGGUUGGUUCCUUGGCCUCUGAUUACCUGGCAAA
..--.......((-(((..(((((((((.(((.....))).)))))))))((((((((....)))))).))--------((((...(((......))).))))........))))).... ( -41.00)
>DroSec_CAF1 101929 118 - 1
UAUAUAAAUACCC-AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUUCGCU-AGGACUCUAGCUCCUUGGCUUCCAGGUUGUUUCCUUGGCCUCUGAUUACCUGGCAAA
...........((-((((((((((((((.(((.....))).)))))))))(((((((.....-))))).))...)))))))...((((((.(((............))).)))))).... ( -43.00)
>DroSim_CAF1 101740 118 - 1
UAUAUAAAUAUCC-AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUUCGCC-AGGACUCUGGCUCCUUGGCUUCCAGGUUGUUUCCUUGGCCUCUGAUUACCUGGCAAA
...........((-(((....(((((((.(((.....))).)))))))(((((((....(((-((....)))))..(((((...)))))..........))))))).....))))).... ( -43.60)
>DroEre_CAF1 104438 97 - 1
UA--UAAAUAUCCAAGGGACUUGGUCGACUUGUUUCUCAACUUGGCCAGGAGC---------------------UCCUUUGCUUCCAGGUCGCUUCCUUGGCCUCUGAUUACCUGGCAAA
..--........((((((((((((((((.(((.....))).))))))))).((---------------------.(((........)))..)))))))))(((...........)))... ( -28.70)
>DroYak_CAF1 106031 98 - 1
UA--UAAAUAUCCCAGGGACUUGGUUGACUUGUUUCUUAACUUGGCCAAGAGG------------G--------ACCCUGGCUUCCAGGUCGUUUCCUUGGCCUCUGAUUACCUGGCAAA
..--........(((((.....((((((........)))))).(((((((.(.------------.--------(((((((...)))))..))..))))))))........))))).... ( -34.40)
>DroAna_CAF1 101284 94 - 1
----UAAAUAUCC-AGAGACGUAUUCAAUUUGUUUCCCAACAUGGCCAGAAGGUCCUU--------------------UGGCAUCGACG-GGCAUCCUUGGCCAUUGAUUACCUGGCAAA
----.......((-((....(((.((((..((((....))))(((((((...((((.(--------------------((....))).)-)))....))))))))))).))))))).... ( -25.30)
>consensus
UA__UAAAUAUCC_AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUU_______G________UCCUUGGCUUCCAGGUUGUUUCCUUGGCCUCUGAUUACCUGGCAAA
...........((.(((..(((((((((.(((.....))).))))))))).............................((((...(((......))).))))........))))).... (-21.24 = -21.97 +   0.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,084,838 – 2,084,935
Length 97
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 66.79
Mean single sequence MFE -24.44
Consensus MFE -9.82
Energy contribution -11.72
Covariance contribution 1.89
Combinations/Pair 1.26
Mean z-score -1.69
Structure conservation index 0.40
SVM decision value 0.29
SVM RNA-class probability 0.670196
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2084838 97 - 22407834
GUUUAAAGGAAUAUUGAGAGAAAAA--------UAAUA--UAAAUAUCC-AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUUUGCAAAGGACUCU--------G
.......(((.((((..........--------.....--..)))))))-.....(((((((((.(((.....))).)))))))))((((((((....)))))).))--------. ( -27.33)
>DroPse_CAF1 136828 100 - 1
AAUGAAAGGAAC---GAAAGGAAUCCUUGAGGA-AAAA--UAAAUAUCU-AGCGACGUUUCAAAUUUGUUUCUCAAGUUAGUU-GGAGCUCCUUUAG-------CCUUGGUC-CAG
.....((((...---.((((((.(((....)))-....--......(((-(((((....)).((((((.....)))))).)))-)))..))))))..-------))))....-... ( -20.90)
>DroSec_CAF1 101969 106 - 1
GUUUAAAGGAAUAUUGAAAGAAAAA--------UAAUAUAUAAAUACCC-AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUUCGCU-AGGACUCUAGCUCCUUG
.....(((((...............--------................-((((((((((((((.(((.....))).)))))))...))))))).(((-((....)))))))))). ( -32.10)
>DroSim_CAF1 101780 106 - 1
GUUUAAAGGAAUAUUGAAAGAAAAA--------UAAUAUAUAAAUAUCC-AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUUCGCC-AGGACUCUGGCUCCUUG
.....(((((...............--------................-((((((((((((((.(((.....))).)))))))...))))))).(((-((....)))))))))). ( -34.10)
>DroYak_CAF1 106071 86 - 1
GUUUAAAGGAAUAUUGAAAGAAAAA--------UAAUA--UAAAUAUCCCAGGGACUUGGUUGACUUGUUUCUUAACUUGGCCAAGAGG------------G--------ACCCUG
.......(((.((((..........--------.....--..)))))))(((((.((((((..(.(((.....))).)..))))))...------------.--------.))))) ( -18.23)
>DroAna_CAF1 101323 80 - 1
GUUUAAAGGAAUCUUUUAAGAAAAA---------------UAAAUAUCC-AGAGACGUAUUCAAUUUGUUUCCCAACAUGGCCAGAAGGUCCUU--------------------UG
...(((((((.((((((........---------------.........-.((((((.........))))))((.....))..)))))))))))--------------------)) ( -14.00)
>consensus
GUUUAAAGGAAUAUUGAAAGAAAAA________UAAUA__UAAAUAUCC_AGGGACUUGGCCGACUUGUUUCGCAACUUGGCCAGGAGGUCCUU_GC____G__UCU___UC__UG
.....(((((....................................((.....))(((((((((.(((.....))).)))))))))...)))))...................... ( -9.82 = -11.72 +   1.89)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:44 2006